The pheromone‐based control of the invasive tomato pinworm Tuta absoluta (Lepidoptera: Gelechiidae) has been unsatisfactory in some cases, and parthenogenesis was reported in this species. As the parthenogenesis phenomena is a shortcoming that compromises the pheromone‐based control of T. absoluta and that is potentially explained by the occurrence of the endosymbiont Wolbachia in this pest species, the objectives of this study were (i) to survey the Wolbachia strains in Brazilian pinworm populations, (ii) to assess the genetic diversity in the tomato pinworm, and (iii) to determine whether parthenogenesis does occur associated with the most representative combination of insect haplotype and Wolbachia strain. The 10 insect populations were infected with two Wolbachia strains (ST41 and ST354), with infection rates ranging from 70% to 100%. The insect genetic diversity was low with a single haplotype group present for both mitochondrial and nuclear DNA markers. The most representative combination of pinworm‐Wolbachia produced 6.88 ± 1.70 eggs per unmated female, all of which were inviable. Thus, Wolbachia infection does not lead to either parthenogenesis or pheromone‐based control failure among Brazilian populations of the tomato pinworm, but likely favours cytoplasmic incompatibility, which is also potentially useful as a pest management tool.